Hidden Scars
by N7-SpaceHamsters
Summary: This story takes place just after ME3 where Shepard chooses the destroy ending. She is trying to get everything back to the way things were before but the Reapers didn't just scar planets. When unsettling truths are brought to light Shepard is forced to face what could be the hardest decision of her entire career.
1. I

I closed my eyes as the burning heat engulfed me, the pain I had been fighting now felt like nothing compared the searing burn that entangled me. As the pain reached its peak it all suddenly stopped. Everything stopped. When I opened my eyes I was no longer on the Citadel. I saw gray in all defections only broken up by ghostly blackened trees and hazy black shadows. The shadows whispered to me but their words were to quite to hear but they sounded familiar like I knew who was speaking. Like I had heard their words before. I felt something looming at my side and I looked down at a lone bench, the same dark color as the trees. I walked behind it and ran the edge of my fingers along the back of the splintering wood. It felt strange, like when a part of your body is asleep and everything you touched to is dulled. I walked around to the front of the bench and took a seat, not knowing why just that it seemed right. I knew where I was and how I had gotten there. This seemed different from the last time. Last time death had been my end, there had been no world after my eyes shut for the final time but that might have been because I wasn't dead for long. I wasn't meant to see the other world, unlike this time. I leaned back on the bench and crossed my arms over my chest as I looked at the shadows trying to understand their gentle whispers.

"Hey Skipper," A voice said clearly catching me off guard, I turned on the bench quickly looking to the owner of the voice as they approached the bench. Ashely, came and joined me. She stared out at gray void tangled with trees. I just I looked at my former crewmate with a deepening sadness. Seeing her again after all this time reminded me how young Ashely had been when she died. So young and brave and she was damn determined all of that was lost to the world when I left her behind on Virmire. I hated myself for doing that, it had been her or Kaidan and as terrible as it might have been I didn't need to think about the choice for long. Ashley had been one of my crew mates and over the time we had spent together we had grown to be close friends but Kaidan was something else, more than a friend. I loved him.

Ashely looked over at me to see my shocked and heartbroken expression. She shook her head.

"I got to say, Shepard, you look like shit." I chuckled and looked down at my arms, my burns were still there, skin blackened and charred. But the pain wasn't there anymore. Just like when I touched the bench everything somehow felt numb.

"Reaper lasers aren't gentle," I said, she chuckled and I was suddenly reminded of our late night conversations in the mess hall, just shooting shit over a beer if we could find one. She had made many of my sleepless night more bearable with hardy conversation and the presence of a friend.

"Are the others okay?" I asked nervously await her answer as I turned my hands over in one another.

"If they weren't," She said raising her hands to either side "They'd be here." She said dropping her arms back in place and slouching onto the bench. I relaxed and mimicked her, looking around almost waiting for something to change.

"I thought it be different," I said letting my worry fall away.

"How so?" She asked eyebrows raised as she looked over at me with the slightest turn of her neck.

"I don't know, brighter maybe. I was hoping to see people." I said and she cocked her head to the side inviting me to go on.

"You," I said nodding at her, "Mordin, Thane, Jenkins," I paused for just second "My dad."

"Well, I hate to break it to you Shep, but this isn't heaven." I looked over at her surprised. Ashley had been one of the very few people I had encountered on my travels that shared my belief of God and the world after death.

"What do you mean?" I asked my voice taking on an edge of the worry I had since let go of. A hand dropped on my shoulder from behind me. I turned around quick I was started to find Mordin standing there, his large black eyes pooling with empathy.

"Time is up, Shepard." He said softly, I turned to looked at Ash again but she was gone I quickly turned back to Mordin and he too, gone. I heard Ash's voice in my head as nothing more than a soft whisper no louder than the black shadows, only unlike the shadows I understood her words.

"Tell the others I say hi." Then everything came crashing away, the sweet numbed feelings disappeared and were replaced with pain unlike that I had ever felt before. I saw black and felt my eyes were shut, I struggled to pull them open; I was face down on the ground. I took a deep breath but felt like my lungs were being crushed by some immense force that was pushing down on my body. I tried to move my arms, pain broke out over the dead flesh that now coated them. Every second I spent with my eyes open felt like a battle, my body wanting nothing more than to lay there unmoving and retune to that world of gray and numbness. This hurt so much. But thoughts of my crew, of my friends, of Kaidan, came to mind and I fought the pain until I could reach my omi-tool and send out a distress signal. When I was done I let my arms fall still once more. I tried to control my breathing but something was crushing me, I couldn't see or really feel what it was but something was there. I tried to move in any way I could and one leg scraped the ground with burning pain, the other I couldn't move. I didn't even know if it was still there. Everything hurt too much for me to tell one pain from another. There was a warm ooze pooling around my body and pain accompanied by the sticky warmth of blood at my core. No matter how hard I fought the blackness came creeping into the edge of my vision and I willed myself not to pass out.

I thought I had succeeded, waiting there in agony for what felt like an eternity; battling pain, unable to move. When I opened my eyes again I found that I had lost my battle of conciseness and was no longer being crushed but moved somewhere fast. My mind overwhelmed I tried to look around unsure of what was happening. Everything was a blur of motion and sound. As I struggled to breathe I heard a voice beside me speak.

"Hang in there Shepard, we're going to get you help." I knew this voice, it was the voice of a friend but with my thoughts so loosely strung together and pain control everything I did, thought or felt I couldn't place who the voice belonged to; not until I heard the voice as a loud course of swearing and shouting at everyone and anyone but myself. Jack. I knew she actually liked me somewhere deep down past that rugged tattooed exterior. I would have smiled if I had had the energy. But before I could stop myself the world and my blurred vision turned to black again and I felt nothing but pain, passing out was suppose to stop the pain. It didn't.

 **AN/ Thank you all so much for reading this, I really enjoy writing it and would love to hear your feedback. Sorry if there is any grammar or spelling problems, editing isn't really my strong suite.**


	2. II

**A/N- So here's a chapter I've been sitting on for awhile. I've been debating whether or not to write another story going over the events of the ME trilogy. If you lovely readers have any thoughts and opinions I'd love to hear them. Please review and comment they are greatly appreciated.**

The next time I found the energy to open my eyes I would have thought I was dead if it hadn't been for the subtle but constant beeping. Everything was blurry, things felt slower and numbed. As my sense slowly took hold again I felt an excruciating pain in my abdomen, but nothing like the pain I last remembered. It burned and radiated out from a single spot to every part of my body. I waited for my eyes to clear and I heard the beeping starting to become quicker. I saw the roof was dark gray and slowly I turned my head, I was in a hospital room. The door to the room quickly opened and there were several sets of footsteps that come flooding in and I was soon greeted by voices that were foreign to me. I had done little more than move my head but theses people seemed worried. A woman came to looked down at me, she shined a flashlight in my eyes, I squinted them shut fast and tried to bring one hand up to shield myself from the bright light. I couldn't find the strength to speak, my mind felt foggy and lulled.

"She's responsive," The woman said shoving the pen light back into the pocket on her white coat. She leaned back over to looked at me this time as a person and not a subject.

"Hello Commander, you're at a hospital on earth, you've been in a coma for a couple of weeks. You're going to be weak for a little while because of it. The pain medication we have you on is also going to make things difficult to understand at this time. You're probably best to try and get some rest for now until we can ease you off the medication." I looked up at her, I had been in a coma, for how long? What was the state of things? Despite my questions, I nodded and leaned my head back giving into the nagging burn of my tired eyes.

I wasn't sure how long I was asleep for but I woke up what felt like seconds later, my eyes stilled burned with a longing for sleep. But this time my body hurt less, there was still pain but it was far more bearable than before. I looked around this time finding the energy to move around a little. I lifted both my arms into the air remembering the pain and now feeling a terrible itch in them. I found them bound with many layers of bandage. I used my bound arms to lift myself a little it hurt to bend but I now had a clear view of the room as I sat up. I was surprised when I looked over and found a sleeping woman doubled over in a chair beside me. I knew who she was the second I saw her, she was older with blond hair the same colour as mine only streaked heavily with gray. Her head lolled over into her shoulder and her eyes were closed. I smiled, it had been quite some time since I had seen my mother, I had worried about her every day of the war, even after Anderson confirmed her safety. with a tug on the wires buried under my bandages found I was still hooked up to that beeping machine, it beeped with every beat of my heart. The room itself was bland, there was little more than a table in the corner with a single chair tucked into it. I felt a perching pain in my side growing worse, I ignored it. I lifted the blanket that was wrapped around me. I wore a stander issue hospital gown and as I lifted the paper thin fabric I found my stomach wrapped with another thick layer of badge just like my arms. Having inspected the closer of my wounds I lifted the blanket off my leg and felt fear grip me tighter than any pain could. Large metal pins were sticking out of my leg all connected to three metal circles keeping them in place going up the length of my leg.

I stared at it horrified and was momentarily distracted when the chair beside me creaked as someone moved, my eyes were torn from the mess of metal and flesh that was my leg and I looked at my tired mother.

"Jane." My mother said sweeping her fair hair out of her eyes. "You're awake." She looked so tired but she smiled at me with relieved eyes.

"Mom," I said sounding almost surprised. "How long have you been waiting for me to wake up?"

"Too long," She said with a faint smile as she adjusted herself to better look at me from her chair. I tried to pull myself up a little high and felt the metal pins in my leg catch on the soft fabric of the bed. My attention was drawn back to my wounds.

"What happened to my leg?" I asked my voice horse and thick from my long sleep. My mothers smiled faded as she to looked down at my leg. There were long scars that traced around my leg and I caught the faint glow of cybernetic beneath them.

"You were caught under some rubble on Citadel when the crucible fired, your leg took the worst of it." She looked back up to meet my worried eyes. She gave a heavy sigh, "I don't know all the medical terms but that thing," She said nodding her head at the metal. "It's supposed to help keep things in place. I'll let the doctor explain." I nodded still horrified at this thing that made me appear almost synthetic, I suppose with all the cybernetics I had I was closer to synthetic than organic anymore. I took a moment to stare at the metal for a second longer before I looked away back my mother.

"What happened? You said the crucible fired, did it work?" She smiled and nodded several times.

"Yes, it worked. The Reapers have been destroyed." I let out a sigh of relief and closed my eyes to savor the knowledge. There had been many losses but at least they were not lost in vain now, their sacrifice meant something. The galaxy was safe.

"And my crew? The Normandy? Are they okay?" She had to sit to think about this for a moment. Ashley had told me they were alright in my dream or vision or whatever that had been but I needed to know for sure.

"From what I've gathered from the new vids the Normandy crashed as it tried to escape the blast from the mass relays." I felt my heart stop and I heard nothing but the word crashed over and over. She had said it so simply there must have been more, it couldn't be that bad, could it? She looked over when she heard the beeping of my heart rate getting louder and faster as the machine alerted everyone in the room of my fear.

"Oh no, they're all okay, no one died," Said lifting her hands quickly trying to clarify what happened to calm me down. "They landed on a foreign planet, they're okay." I nodded taking a few deep breaths trying to calm myself down. My mother picked up a bag from beside her chair and rifled through it until she pulled out a datapad.

"I saved an article about it, I'll try and find it." She said tapping on the yellow screening in a hurry, she probably felt bad for worrying me. The door to the room opened a few seconds later as I smiled at my mother's skill navigation through what was surely a mess of files on the datapad, a lean red haired woman walked in the room.

"Commander Shepard, your awake." Said the woman I now recognized from the first time I woke up, she had been the one with the flashlight. My mother stopped scrolling through the datapad and smiled as the doctor entered.

"How are you feeling?" The woman asked when I didn't respond.

"Good," I lied, fighting both the pain and the drowsy feelings. She reminded me of Miranda, the way she carried herself like she was superior to others.

"Excellent, now I'm sure you're quite curious about your condition." She said gesturing down to the strange state of my leg. I nodded awaiting her answer.

"As I told you last time, though I doubt you remember it, you've been in a coma for quite some time." She came to stand next to the bed between my mother and me.

"How long exactly?"

"Nearly three months. Your wounds were extensive and it was the right course of actions regarding your recovery."

"Wait, you put me in the coma?" I asked sharply, I had been in a coma for nearly two years once before while Cerberus rebuilt me, theses people seemed to be doing it again. A small amount of regret or guilt came over the doctor's pale face.

"Yes, it was a medically induced coma, I understand this might be unsettling but your injuries were very severe. Commander, I doubt you would have made the recovery you have without it. Not to mention the pain you would have suffered would have been unbearable, with that of skin graphs and your adnominal wound." I nodded and looked down at my hands as they tightly gripped my bandaged core.

"What are the full extent of my injuries?" I asked my eyes once again locked on my leg, this could ruin me and my career forever. Please tell me it won't ruin me. I need to still be a soldier. I thought, doing everything but physically begging the doctor for a good outcome.

"You suffered third-degree burns to your arms, legs, and torso. These burns made it difficult to close wounds like the one on your abdomen, due to the fact that your stitches kept ripping from the burned skin. Skin graphs were done and various cybernetics were implanted. You also sustained a large abdominal puncher that went right through to further disrupt your liver and kidneys. It took a few long hours of surgery but thanks to our brilliant team of doctors we repaired the damage. You are unfortunately down to one kidney now and were suffering some an infection a few weeks ago, it was taken care of with a few rounds of antibiotics. Unfochently the wound itself is still healing and your stitches can be removed in a few days. Your leg is the worst of injuries, your fibula and tibia were both completely crushed and there was no viable bone to be found. We inserted metal rods inside your leg to make up for the lost bone material, those pins are there to try and keep everything in place and together while your bone heals to the rods. There was also a great loss of muscle and tissue in the area, we were able to fix most of it but a lot of the damage you sustained will be irreversible."

"What does the mean for me?" I asked my heart being to grow faster, the beeping from the machine alerting the others. I willed myself to remain calm. But I couldn't just keep the brave face, my heart rate was selling me out.

"You will have limited mobility in your leg from what I can assume will be the rest of your life." She sounded solum as she shared the grim news, she had to know what this would do to me.

"Anything else?" I asked tightly, trying to control my pounding heart and sooth the fear that had flooded my chest.

"You'll have many scars from the burns, but with more surgery, those can be made less noticeable. Other than that you should make a healthy recovery." I dropped my eyes to anything but my leg, but my arms or any of my wonders. I felt all eyes on me so I straightened up looked at the doctor with the most unfazed look I could manage.

"How long until I can retune to duty?" The lean woman's eyebrows shot up in surprise, she looked over to my mother fast, my mother just shook her head and gave a small smile. The doctor looked back to me and spoke,

"I'm sorry Commander but with your injuries, I wouldn't recommend a retune to active duty. Perhaps a job here on earth but not field work." I nodded.

"And your recommendations have been noted. But with all due respect doctor, I've seen soldiers with worse injuries than a few burns and broken bones back on their feet and into battle in the time I've spent sleeping."

"Commander Shepard, you have much more than a few burns and broken bones. It's a miracle we were able to save your leg at all. When they found you in the rubble you were black tagged, had it not been for who you were and what you've done you would be dead."

"I can't be the first of your patients to go against recommendations," I argued trying not to face what she had just said.

"No you are not but if you wish to make a proper recovery I highly recommend you stay away from active duty."

"You said I should make a healthy recovery regardless,"

"Yes but you could make the state of your leg worse by using it too much in a combat situation, you are also at risk of damaging your only remaining kidney, and further damaging your liver."

"I thought you said my internal damage was repaired?"

"It was, your organs were damaged, we repaired the damage but they are scared like the rest of you. If you are even hit too hard the damage to your liver could be irreversible. If that came to pass you would then need a transplant or more surgery. You've sustained enough damage for two lifetimes, you're incredibly lucky to still be alive. I'll need you to…" The doctor trailed off as shouting came from outside the door. It cut through the walls clear as if the fighting pair were inside the room.

"Ma'am you can't go in there. The doctor-" A meek voice pledged.

"The doctor can kiss my ass." I heard a very familiar voice bark. I couldn't help but smile as the door to the room was roughly thrown open and Jack walked in the room with a fast confident pace. The doctor turned and cast a worried and surprised look at the small fully tattooed woman.  
"Well, would you look at that, sleeping beauty finally woke up." Jack mocked as I just smiled at her.

"Ma'am, you can't-" The woman from the hallway came fumbling into the doorway the doctor just lifted one hand to the woman.

"It's alright, leave her be." The doctor said before lifting her annoyed gaze from the ground.

"We will talk again later, Commander." The doctor then walked from the room and shut the door behind her, casting a glare at Jack.

"Thanks for that," I said nodding toward the door where the doctor has just gone out.

"Yeah, that doctor chick is an uptight bitch, she's tried to stop me every time I've come to see you. Never works, though." She said leaning against the wall beside the small window, a large smirk stretched across her face.

"You came to see me?" I asked poking at her in a way I knew she would be annoyed with.

"Had to come make sure your ass wasn't dead every once in awhile,"

"Jacks been good company, helped me keep my card skills sharp." My mother said and I turned to looked at her surprised, she and Jack must have made themselves acquainted in my absents.

"Yeah, your mom's even smarter than you. And I thought I had seen the best and brightest of the Shepard line." Jack said with fake praises.

"The best and brightest?" I questioned.

"You stopped the Reapers, don't let it go to your head. Besides you always sucked at cards." I smiled recalling one of the many times I had lost more than a few credits to Jack in our many card games with the crew.

"Maybe my new implants will help with that," I said jokingly as I gesturing to the glow beneath my skin. She laughed and shook her head.

"You can't get card skills through cybernetics," She teased.

"You can't teach it either," My mother said, setting her datapad down on her lap "Lord knows I've tried to teach you." I looked at her with fake hurt but I couldn't hide my smile and I heard Jack snicker as she walked over to the foot of my bed.

"Speaking of teaching, how are your students?" I asked shifting my gaze back to my former crew member. She shrugged,

"They were a little sore after the whole Reaper invasion thing, but I whipped their asses into shape, they're even eager to get back into action, they want to work with you once your able." I sighed and looked down at my leg moving it a little feeling the metal push and pull against my skin.

"I think that might be awhile," I said not returning my gaze to either of the others in the room.

"Better not, you've got one hell of a fucking mess to clean up, Shepard."

Jack stayed for the remainder of the day. After my mother left to go get something to eat Jack told me that my mother had been here every day, during my coma she came in daily to check on me. Jack she often came in and found her explain different ships schematics to me. She also told me more about the state of the Normandy and my crew. It hadn't taken them long to get the ship up and running after the crash, but without the mass relays, it was a longer flight back to earth. The ships arrive time about two weeks. She also said they had been informed of my miraculous survival and that they wanted to see me as soon as they landed. I didn't think I could be so excited to see a group of people, just hearing that they were okay seemed to make all my pain much easier. Later that day as the evening begun to take over my mother and Jack talked me into a round of cards, and just as Jack was clearing my mother and me of our spear credits in a game of poker the doctor came in and dismissed both my visitors due to the late hour. Jack left but not without give the finger to the doctor and my mother promised to be back in the morning. The doctor waited in the room until both parties had left and turned to look at me.

"How is your pain?" She asked me as she hovered by the end of my bed. I ran a hand across my sore abdomen,

"Great," I lied. I'd damned if I let this bother me. "But the metal rods are a little unsettling, when will they come out?"

"We have you scheduled for an x-ray tomorrow morning to see how your bones are doing. If everything looks good we should be able to remove it within a couple of days."

"And how much longer after that until I'm released?"

"Your arms should be healed and you have no fever or other signs of infection, this leads me to believe you've almost recovered from your abdominal wound. We should be able to remove your stitches soon along with the leg brace. You'll have to complete some minor physical active to prove your legs capability but that shouldn't take much more than a week."

"How would I get cleared for duty?" The doctor once again shook her head and smooth out a loss peace of red hair.

"I suppose that will be up to your commandeering office, I'll submit my report to Admiral Hacket once you have been released."

"Thank you, Doctor." The doctor nodded,

"I should be thanking you, Commander. You did save the galaxy. Now is there anything I can get for you before I leave?" She said kindly, I had to stop and think about why she was thanking me. I saved the galaxy, but it sure as hell didn't feel that way. I was glad the reapers were gone but I wasn't the reason for it being that way, I just pulled the trigger. If it hadn't been for the help of our allies I could never have done that. So it really didn't feel right to hear her hold me as the hero of the galaxy like that. I nodded and gave her a weak smile.

"I'm fine, thank you, doctor," I said wanting nothing more than to get some sleep. I felt exhausted even though I hadn't moved from that bed in the few short hours I had been awake. The red-haired woman smiled before she turned and left the room. I was now alone in this tiny closed off space. I leaned back in the bed letting my aching abdomen rest from constantly sitting up. I was so weak and I hated it. A silver flash caught my attention and I looked to my right at the medium sized window that overlooked the rest of the hospital and the bustling street out front. I had no idea where I was but something about the warm purple glow from further out and the shape of the builds told me I was on the Citadel. I watched the display of speeding cars and all their bright colors until I found myself drifting off to sleep. I almost felt the need to fight it, all those nights on the Normandy willing myself to stay awake and work had trained me to fight sleep; but this time, I gave in and let my tired eyes close. The war was finally over.


End file.
